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Not S4 user but still able to help. Your shift buttons have dedicated modifiers (one for each). I'll give you example of how it works using modifier #1:

For gain command use modifier condition M1=0. Lets assume your shift is using M1 set to hold, this means when you press shift the modifier condition should change from 0 to 1 and on release of shift button value should jump back to zero. Now back to gain command - go in to controller manager, find gain adjust command and set modifier condition to M1=0 which means your gain isn't gonna work as long as shift button is on hold.

Now add in key adjust command and dedicate M1=1. There it is, hold shift, key working - gain is off. Leave shift - back to gains!

I haven't used S4 (ever) but I did look into mapping once and if I remember correctly left shift was M1 and the right one was M2. I'm not aware of new override feature but anyways you should check little modifier slots (1-8) in controller manager. Not sure if this have been hidden too?

You will need to add(not override) a modifier to your shift button. Set it to direct and 1 with a hold action. Then add the key change to the gain knob and select override and select the modifier =1. Then add channel gain to the knob and override and select modifier=0.
You may also need to change the acceleration/sensitivity of the encoder to have it change the values like you want.

You cannot see or actually change the HID mapping for the S4, but you can add to it or override it. You only can see what you map on top of it. Sorta like mapping starting a mapping from scratch (you have all 8 modifiers and their states available to map), but you have to take into account what the stock mapping does and either add a function to the hardware control, or do away with the stock mapping's function(override).

So to make the gain encoders change gain as normal and change key when shift is pressed, we added a modifier to the shift key (making the shift function for your gain/key knob). Then we had to get rid of the gain control the stock mapping uses and remap it using our new modifier so the knob would no longer control gain with the shift key pressed.

I hope that clears things up a bit!

https://maps.djtechtools.com/mappings/842
Here's a mapping I made that adds the key change to the tempo offset buttons, as well as flux, auto gain, and fx1-4 on offs in mixer. This mapping uses the same techniques described above. If you take look at the mapping you can see I added modifiers to the shift buttons, and use it to make the Fx mode button turn flux on and off.